Presence and Persistence of Viable, Clinically Relevant Legionella pneumophila Bacteria in Garden Soil in the Netherlands

What on earth? The impact of digestates and composts from farm effluent management on fluxes of foodborne pathogens in agricultural lands

The recycling of biomass is the cornerstone of sustainable development in the bioeconomy. In this context, digestates and composts from processed agricultural residues and biomasses are returned to the soil. Whether or not the presence of pathogenic microorganisms in these processed biomasses is a threat to the sustainability of the current on-farm practices is still the subject of debate. In this review, we describe the microbial pathogens that may be present in digestates and composts. We then provide an overview of the current European regulation designed to mitigate health hazards linked to the use of organic fertilisers and soil improvers produced from farm biomasses and residues. Finally, we discuss the many factors that underlie the fate of microbial pathogens in the field. We argue that incorporating land characteristics in the management of safety issues connected with the spreading of organic fertilisers and soil improvers can improve the sustainability of biomass recycling.

Presence of Viable, Clinically Relevant Legionella Bacteria in Environmental Water and Soil Sources of China

The distribution of pathogenic Legionella in the environmental soil and water of China has not been documented yet. In this study, Legionella was detected in 129 of 575 water (22.43%) and 41 of 442 soil samples (9.28%) by culture. Twelve Legionella species were identified, of which 11 were disease-associated. Of the Legionella-positive samples, 109 of 129 (84.50%) water and 29 of 41 (70.73%) soil were positive for L. pneumophila, which accounted for about 75% of Legionella isolates in both water and soil, suggesting L. pneumophila was the most frequent species. Soil showed a higher diversity of Legionella spp. as compared with water (0.6279 versus 0.4493). In contrast, serogroup (sg) 1 was more prevalent among L. pneumophila isolates from water than from soil (26.66% versus 12.21%). Moreover, many disease-associated sequence types (STs) of L. pneumophila were found in China. Intragenic recombination was acting on L. pneumophila from both water and soil. Phylogeny, population structure, and molecular evolution analyses revealed a probable existence of L. pneumophila isolates with a special genetic background that is more adaptable to soil or water sources and a small proportion of genetic difference between water and soil isolates. The detection of viable, clinically relevant Legionella demonstrates soil as another source for harboring and dissemination of pathogenic Legionella bacteria in China. Future research should assess the implication in public health with the presence of Legionella in the soil and illustrate the genetic and pathogenicity difference of Legionella between water and soil, particularly the most prevalent L. pneumophila. IMPORTANCE Pathogenic Legionella spp. is the causative agent of Legionnaires' disease (LD), and L. pneumophila is the most common one. Most studies have focused on L. pneumophila from water and clinical samples. However, the soil is another important reservoir for this bacterium, and the distribution of Legionella spp. in water and soil sources has not been compared and documented in China yet. Discovering the distribution of Legionella spp. and L. pneumophila in the two environments may help a deep understanding of the pathogenesis and molecular evolution of the bacterium. Our research systematically uncovered the distributions of Legionella spp. in different regions and sources (e.g., water and soil) of China. Moreover, phylogeny, population structure, and molecular evolution study revealed the possible existence of L. pneumophila with a special genetic background that is more adaptable to soil or water sources, and genetic difference may exist.

Effects of Strigolactone on Torreya grandis Gene Expression and Soil Microbial Community Structure Under Simulated Nitrogen Deposition

Nitrogen enters the terrestrial ecosystem through deposition. High nitrogen levels can affect physical and chemical properties of soil and inhibit normal growth and reproduction of forest plants. Nitrogen modulates the composition of soil microorganisms. Strigolactones inhibits plant branching, promotes root growth, nutrient absorption, and promotes arbuscular fungal mycelia branching. Plants are subjected to increasing atmospheric nitrogen deposition. Therefore, it is imperative to explore the relationship between strigolactone and nitrogen deposition of plants and abundance of soil microorganisms. In the present study, the effects of strigolactone on genetic responses and soil microorganisms of Torreya grandis, under simulated nitrogen deposition were explored using high-throughput sequencing techniques. T. grandis is a subtropical economic tree species in China. A total of 4,008 differentially expressed genes were identified in additional N deposition and GR24 treatment. These genes were associated with multiple GO terms and metabolic pathways. GO enrichment analysis showed that several DEGs were associated with enrichment of the transporter activity term. Both additional nitrogen deposition and GR24 treatment modulated the content of nutrient elements. The content of K reduced in leaves after additional N deposition treatment. The content of P increased in leaves after GR24 treatment. A total of 20 families and 29 DEGs associated with transporters were identified. These transporters may be regulated by transcription factors. A total of 1,402,819 clean reads and 1,778 amplicon sequence variants (ASVs) were generated through Bacterial 16S rRNA sequencing. Random forest classification revealed that Legionella, Lacunisphaera, Klebsiella, Bryobacter, and Janthinobacterium were significantly enriched in the soil in the additional N deposition group and the GR24 treatment group. Co-occurrence network analysis showed significant differences in composition of soil microbial community under different treatments. These results indicate a relationship between N deposition and strigolactones effect. The results provide new insights on the role of strigolactones in plants and composition of soil microorganisms under nitrogen deposition.

Validating a clinical prediction score for Legionella-related community acquired pneumonia

BACKGROUND

Legionella-related community acquired pneumonia (CAP) is a disease with an increasing incidence and a high mortality rate, especially if empirical antibiotic therapy is inadequate. Antibiotic treatment highly relies on clinical symptoms, although proven non-specific, because currently available diagnostic techniques provide insufficient accuracy for detecting Legionella CAP on admission. This study validates a diagnostic scoring system for detection of Legionella-related CAP, based on six items on admission (Legionella prediction score).

METHODS

We included patients with Legionella-related CAP admitted to five large Dutch hospitals between 2006 and 2016. Controls were non-Legionella-related CAP patients. The following six conditions were rewarded one point if present: fever > 39.4 °C; dry cough; hyponatremia (sodium) < 133 mmol/L; lactate dehydrogenase (LDH) > 225 mmol/L; C-reactive protein (CRP) > 187 mg/L and platelet count < 171 × 10⁹/L. The accuracy of the prediction score was assessed by calculating the area under the curve (AUC) through logistic regression analysis.

RESULTS

We included 131 cases and 160 controls. A score of 0 occurred in non-Legionella-related CAP patients only, a score of 5 and 6 in Legionella-related CAP patients only. A cut-off ≥ 4 resulted in a sensitivity of 58.8% and a specificity of 93.1%. The AUC was 0.89 (95% CI 0.86-0.93). The strongest predictors were elevated LDH, elevated CRP and hyponatremia.

CONCLUSIONS

This multi-centre study validates the Legionella prediction score, an easily applicable diagnostic scoring system, in a large group of patients and finds high diagnostic accuracy. The score shows promise for future prospective validation and could contribute to targeted antibiotic treatment of suspected Legionella CAP.

Quantification of pathogens and antibiotic resistance genes in backyard and commercial composts

Compost is widely used for gardening. Growers can choose to buy compost from markets or make compost at home. Potential exposure of users to pathogens through composting includes ingesting foodborne pathogens and inhaling airborne pathogens. This study compared the abundances of the genetic markers of five opportunistic foodborne and airborne pathogens in the backyard and commercial composts, as well as an immature swine mortality compost. We found that ttrC of Salmonella enterica and ftsZ of Escherichia coli were absent from all ready-to-use compost samples. In contrast, the genes of airborne pathogens such as groEL2 of Mycobacterium spp., mip of Legionella pneumophila, and gyrB of Pseudomonas aeruginosa were detected in the backyard and commercial composts. The groEL2 gene of Mycobacterium spp. was detected in all samples, including the control soil. The abundance of gyrB of P. aeruginosa was high in the two backyard composts, and it was higher than those in any other compost samples. The relative abundances of ARGs were significantly lower in backyard composts than commercial composts. We found that ftsZ of E. coli co-existed with multiple single-drug resistant ARGs in the immature swine mortality compost. We also found that mip of L. pneumophila and gyrB of P. aeruginosa co-existed with aminoglycoside resistance genes. Our findings suggest that inhaling airborne pathogens may carry more risk than ingesting foodborne pathogens when applying composts.

Increased risk of Legionella pneumonia as community-acquired pneumonia after heavy rainfall in 2018 in west Japan

INTRODUCTION

Japan experienced a heavy rainfall event from June 28 to July 8, 2018, and many casualties were caused by both heavy rainfall and flooding. Few studies have investigated patients' characteristics and the causative pathogens of community-acquired pneumonia before and after heavy rainfall events. The aim of the present study was to evaluate the causative pathogens and clinical characteristics of hospitalized patients with community-acquired pneumonia before and after the heavy rainfall event using prospective cohort data.

METHODS

The study was divided into two periods: July to November 2013-2017 (before heavy rainfall) and July to November 2018 (after heavy rainfall). The patients' clinical characteristics and causative pathogens before and after the heavy rainfall were investigated. Regarding the causative pathogens, adjustments were made for precipitation and seasonal patterns.

RESULTS

There were no significant differences in the number and clinical characteristics of patients before and after heavy rainfall. However, the frequency of Legionella pneumonia was significantly higher after than before the heavy rainfall event (8.9% vs 3.0%, P = 0.02) and remained significant after adjusting for precipitation and season. Three of 7 Legionella pneumonia patients engaged in reconstruction work and 2 Legionella pneumonia patients had soil exposure.

CONCLUSIONS

An increased risk of Legionella pneumonia after not only rainfall and serious flooding, but also following recovery work or soil exposure should be considered.

Are pathogenic Legionella non-pneumophila a common bacteria in Water Distribution Networks?

The present study analyzes at the national level, the presence of circulating Legionella in the artificial aquatic systems of different facilities of all of them state-owned centers throughout Spain for 12 months. 1754 water samples from various state-owned centers were collected from January to December 2014. Samples were collected from the cooling towers and evaporative condensers (CTC), and water distribution networks such as domestic hot water (DHW), cold water for human consumption (CW), sprinkler irrigation systems (SIS), fire sprinkler systems (FSS), and water from decorative fountains (DF). All these facilities are considered, according to current regulations, as potential amplifying systems for bacteria and possible sources of infection by the generation of droplets and aerosols. The isolation and counting of Legionella in water samples was carried out using microbiological culture following the international normative UNE-EN-ISO 11,731:2007 (ISO 11,731:1998) and UNE-EN ISO 8199:2008 (ISO 8199:2005).The quantification of Legionella colonization, the annual distribution, and the geographical distribution of the Legionella isolates recovered in the water were analyzed. Besides, molecular techniques were used for the characterization of the Legionella non-pneumophila isolates. Legionella was recovered from 15.79% of the analyzed water samples. High colonization was more frequently detected in water samples from CTC, DHW, CW, and DF. Regarding the geographic distribution, positive samples of Legionella were obtained in 14 of the 18 Spanish locations analyzed. Legionella non-pneumophila was the most prevalent and was isolated from water samples from 13 different geographical locations (72%). Legionella anisa and Legionella jordanis were the most frequently non-pneumophila species isolated. Legionella donaldsonii was isolated for the first time in the water distribution networks in Spain. Legionella pneumophila sg 2-14 was detected in 13 locations and Legionella pneumophila sg 1 in 11 locations. Therefore, our study concludes that the presence of Legionella pneumophila and Legionella non-pneumophila species in these systems can be a potential threat to public health and should be examined thoroughly with complementary techniques, such as molecular techniques as a screen for routine diagnosis.

Effects of climate changes and road exposure on the rapidly rising legionellosis incidence rates in the United States

Legionellosis is an infection acquired through inhalation of aerosols that are contaminated with environmental bacteria Legionella spp. The bacteria require warm temperature for proliferation in bodies of water and moist soil. The legionellosis incidence in the United States has been rising rapidly in the past two decades without a clear explanation. In the meantime, the US has recorded consecutive years of above-norm temperature since 1997 and precipitation surplus since 2008. The present study analyzed the legionellosis incidence in the US during the 20-year period of 1999 to 2018 and correlated with concurrent temperature, precipitation, solar ultraviolet B (UVB) radiation, and vehicle mileage data. The age-adjusted legionellosis incidence rates rose exponentially from 0.40/100,000 in 1999 (with 1108 cases) to 2.69/100,000 in 2018 (with 9933 cases) at a calculated annual increase of 110%. In regression analyses, the rise correlated with an increase in vehicle miles driven and with temperature and precipitation levels that have been above the 1901–2000 mean since 1997 and 2008, respectively, suggesting more road exposure to traffic-generated aerosols and promotive effects of anomalous climate. Remarkably, the regressions with cumulative anomalies of temperature and precipitation were robust (R² ≥ 0.9145, P ≤ 4.7E-11), implying possible changes to microbial ecology in the terrestrial and aquatic environments. An interactive synergy between annual precipitation and vehicle miles was also found in multiple regressions. Meanwhile, the bactericidal UVB radiation has been decreasing, which also contributed to the rising incidence in an inverse correlation. The 2018 legionellosis incidence peak corresponded to cumulative effects of the climate anomalies, vast vehicle miles (3,240 billion miles, 15904 km per capita), record high precipitation (880.1 mm), near record low UVB radiation (7488 kJ/m²), and continued above-norm temperature (11.96°C). These effects were examined and demonstrated in California, Florida, New Jersey, Ohio, and Wisconsin, states that represent diverse incidence rates and climates. The incidence and above-norm temperature both rose most in cold Wisconsin. These results suggest that warming temperature and precipitation surplus have likely elevated the density of Legionella bacteria in the environment, and together with road exposure explain the rapidly rising incidence of legionellosis in the United States. These trends are expected to continue, warranting further research and efforts to prevent infection.

Legionellosis Caused by Non-Legionella pneumophila Species, with a Focus on Legionella longbeachae

Although known as causes of community-acquired pneumonia and Pontiac fever, the global burden of infection caused by Legionella species other than Legionella pneumophila is under-recognised. Non-L. pneumophila legionellae have a worldwide distribution, although common testing strategies for legionellosis favour detection of L. pneumophila over other Legionella species, leading to an inherent diagnostic bias and under-detection of cases. When systematically tested for in Australia and New Zealand, L. longbeachae was shown to be a leading cause of community-acquired pneumonia. Exposure to potting soils and compost is a particular risk for infection from L. longbeachae, and L. longbeachae may be better adapted to soil and composting plant material than other Legionella species. It is possible that the high rate of L. longbeachae reported in Australia and New Zealand is related to the composition of commercial potting soils which, unlike European products, contain pine bark and sawdust. Genetic studies have demonstrated that the Legionella genomes are highly plastic, with areas of the chromosome showing high levels of recombination as well as horizontal gene transfer both within and between species via plasmids. This, combined with various secretion systems and extensive effector repertoires that enable the bacterium to hijack host cell functions and resources, is instrumental in shaping its pathogenesis, survival and growth. Prevention of legionellosis is hampered by surveillance systems that are compromised by ascertainment bias, which limits commitment to an effective public health response. Current prevention strategies in Australia and New Zealand are directed at individual gardeners who use potting soils and compost. This consists of advice to avoid aerosols generated by the use of potting soils and use masks and gloves, but there is little evidence that this is effective. There is a need to better understand the epidemiology of L. longbeachae and other Legionella species in order to develop effective treatment and preventative strategies globally.

Environmental sources of community-acquired legionnaires' disease: A review

BACKGROUND

Most Legionnaires' disease in the US and abroad is community-acquired and believed to be sporadic, or non-outbreak associated. Most patients are exposed to numerous water sources, thus making it difficult to focus environmental investigations. Identifying known sources of sporadic community-acquired Legionnaires' disease will inform future sporadic Legionnaires' disease investigations as well as highlight directions for research. The objective is to summarize and rank sporadic Legionnaires' disease sources based on the level of linkage between the environmental source and cases.

METHODS

A PubMed search was conducted using the search terms legion* and (origins or source or transmission) and (sporadic or community-acquired). Studies of nosocomial and/or outbreak-associated disease were excluded from this review. Definite, probable, possible and suspect ranks were assigned to sources based on evidence of linkage to sporadic Legionnaires' disease.

RESULTS

The search yielded 196 articles and 47 articles were included in the final review after application of exclusion criteria. A total of 28 sources were identified. Of these, eight were assigned definite rank including residential potable water and car air-conditioner water leakage. Probable rank was assigned to five sources including solar-heated potable water and soil. Possible rank was assigned to nine sources including residential potable water and cooling towers. Suspect rank was assigned to 20 sources including large building water systems and cooling towers.

CONCLUSION

Residential potable water, large building water systems and car travel appear to contribute to a substantial proportion of sporadic Legionnaires' disease. Cooling towers are also a potentially significant source; however, definitive linkage to sporadic cases proves difficult. The sources of sporadic Legionnaires' disease cannot be definitively identified for most cases.

Differences in Virulence Between Legionella pneumophila Isolates From Human and Non-human Sources Determined in Galleria mellonella Infection Model

Legionella pneumophila is a ubiquitous bacterium in freshwater environments and in many man-made water systems capable of inducing pneumonia in humans. Despite its ubiquitous character most studies on L. pneumophila virulence focused on clinical strains and isolates from man-made environments, so little is known about the nature and extent of virulence variation in strains isolated from natural environments. It has been established that clinical isolates are less diverse than man-made and natural environmental strains, suggesting that only a subset of environmental isolates is specially adapted to infect humans. In this work we intended to determine if unrelated L. pneumophila strains, isolated from different environments and with distinct virulence-related genetic backgrounds, displayed differences in virulence, using the Wax Moth Galleria mellonella infection model. We found that all tested strains were pathogenic in G. mellonella, regardless of their origin. Indeed, a panoply of virulence-related phenotypes was observed sustaining the existence of significant differences on the ability of L. pneumophila strains to induce disease. Taken together our results suggest that the occurrence of human infection is not related with the increased capability of some strains to induce disease since we also found a concentration threshold above which L. pneumophila strains are equally able to cause disease. In addition, no link could be established between the sequence-type (ST) and L. pneumophila pathogenicity. We envision that in man-made water distribution systems environmental filtering selection and biotic competition acts structuring L. pneumophila populations by selecting more resilient and adapted strains that can rise to high concentration if no control measures are implemented. Therefore, public health strategies based on the sequence based typing (STB) scheme analysis should take into account that the major disease-associated clones of L. pneumophila were not related with higher virulence in G. mellonella infection model, and that potential variability of virulence-related phenotypes was found within the same ST.